Rw4G010780

U5 small nuclear ribonucleoprotein 40

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr4
OG0012055
Physical Location & Seq
Forward (+)
25233184 .. 25236400
3217 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw4G010780.1

Sequence Viewer

Length: 1044 bp
ATGATGCAGTTTGCTCCAAGTGAGGGTGAAAATGCTTTGTCTGTAGTTGGTCCCAGGCCATTGGATTTGTCTACATATAATGCTCGCCCTGCATCTGGGCCTAATGGAAAACAAAGGACGTCAAGTTTGGAGGCACCAATCATGCTGCTGACTGGTCATCAAAGTGCTATATACACAATGAAATTTAACCCTACCGGAACAGTCATAGCATCGGGGTCTCACGACAAGGAAATTTTCTTATGGAATGTTCATGGGGAATGCAAAAACTTCATGGTTTTAAAGGGGCATAAGAATGCTGTGTTGGATCTTCACTGGACAACTGATGGGTCTCAGATAGTATCAGCCAGTCCAGACAAAACTGTGGGGGCATGGGATGTTGAGACGGGAAAAAGAATTAAAAAGATGGCAGAACACTCTTCATTTGTGAATTCTTGTCATCCTGCTCGGAGAGGACCGCCTCTTGTTGTCAGTGGATCTGATGATGGAACTGCCAAACTATGGGATATGCGTGTGAGGGGTGCCATCCAAACATATCCTGATAAATACCAAATCACAGCAGTCAGCTTCTCGGATGCATCAGATAAAATCTTTACAGGAGGTATTGATAATGATATTAAGGTTTGGGACTTGCGCAAGGCTGAAGTACTGATGACACTTCAAGGACATCAAGATATGATAACAGGTATGTCATTGAGTCCTGATGGCTCTTATCTTCTGACTAATGGAATGGACTGCAAACTCTGCATTTGGGATATGCGCCCGTATGCACCACAAAATCGTTGTGTAAAGATAATGGAAGGGCACCAACACAACTTTGAAAAGAACTTGTTGAAATGTAGCTGGTCACCTGATGGAAGCAAGGTCACGGCCGGCAGTTCTGATAGGATGGTCTACATATGGGATACTACTTCTCGACGCATCTTGTTTATGCTGCCGGCCACACTGGATCTGTCAATGAGTCTGTCTTCCACCCCAACGAGCCCATTATTGGATCTGGCAGTAGTGATAAGCAGATATATCTGGGGGAAATCTGAGTTTTACTGA

Protein Analysis

347

Amino Acids

38.39

Weight (kDa)

7.66

Isoelectric Point (pI)

32.82

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Beta-prop_Aladin PF25460 39 - 128 9.6e-07 Aladin seven-bladed propeller
EIF3I PF24805 46 - 253 7.7e-22 EIF3I
Beta-prop_TEP1_2nd PF25047 46 - 145 6.2e-15 TEP-1 second beta-propeller
WD40 PF00400 46 - 82 1.6e-08 WD domain, G-beta repeat
Beta-prop_WDR3_1st PF25173 47 - 169 5.5e-28 WDR3 first beta-propeller domain
WD40_CDC20-Fz PF24807 47 - 100 6.7e-06 CDC20/Fizzy WD40 domain
WD40_Prp19 PF24814 49 - 218 2.4e-25 Prp19 WD40 domain
Beta-prop_WDR5 PF25175 50 - 330 6.4e-58 WDR5 beta-propeller domain
Beta-prop_CAF1B_HIR1 PF24105 50 - 170 3.3e-15 CAF1B/HIR1 beta-propeller domain
WD40_WDHD1_1st PF24817 50 - 137 1.2e-11 WDHD1 first WD40 domain
Beta-prop_WDR36-Utp21_1st PF25171 51 - 164 1.7e-07 WDR36/Utp21 first beta-propeller
Beta-prop_EML_2 PF23414 51 - 137 5.7e-15 Echinoderm microtubule-associated protein second beta-propeller
Beta-prop_THOC3 PF25174 53 - 331 3.7e-49 THOC3 beta-propeller domain
Beta-prop_EML PF23409 53 - 135 3.9e-06 Echinoderm microtubule-associated protein first beta-propeller
WD40_MABP1-WDR62_2nd PF24782 54 - 167 5.7e-07 MABP1/WDR62 second WD40 domain
WDR55 PF24796 54 - 180 1.1e-18 WDR55
WD40_Gbeta PF25391 57 - 301 7.5e-22 G protein beta WD-40 repeat protein
Beta-prop_WDR41 PF25178 67 - 144 1e-06 WDR41
Beta-prop_WDR3_2nd PF25172 87 - 177 5.7e-08 WDR3 second beta-propeller domain
WD40_CDC20-Fz PF24807 91 - 250 8.7e-24 CDC20/Fizzy WD40 domain
WD40_Prp19 PF24814 143 - 312 2.7e-23 Prp19 WD40 domain
Beta-prop_EML_2 PF23414 153 - 304 4.8e-15 Echinoderm microtubule-associated protein second beta-propeller
Beta-prop_WDR3_2nd PF25172 154 - 251 6.6e-13 WDR3 second beta-propeller domain
Beta-prop_WDR36-Utp21_2nd PF25168 154 - 253 4.8e-11 WDR36/Utp21 second beta-propeller domain
Beta-prop_WDR3_1st PF25173 155 - 271 1.9e-19 WDR3 first beta-propeller domain
Beta-prop_WDR36-Utp21_1st PF25171 155 - 269 8.2e-10 WDR36/Utp21 first beta-propeller
Beta-prop_WDR90_POC16_2nd PF23393 157 - 253 2.7e-08 WDR90/POC16, second beta-propeller
Beta-prop_EML PF23409 181 - 310 3.2e-07 Echinoderm microtubule-associated protein first beta-propeller
WD40_WDHD1_1st PF24817 183 - 265 3.4e-11 WDHD1 first WD40 domain
Beta-prop_CAF1B_HIR1 PF24105 184 - 265 2.1e-09 CAF1B/HIR1 beta-propeller domain
EIF3I PF24805 185 - 303 7e-07 EIF3I
Beta-prop_SCAP PF24017 190 - 305 1.2e-06 SCAP Beta-propeller
WDR55 PF24796 194 - 302 9.2e-12 WDR55
WD40 PF00400 215 - 251 1.7e-08 WD domain, G-beta repeat
Beta-prop_TEP1_2nd PF25047 216 - 304 1.6e-08 TEP-1 second beta-propeller
Beta-prop_Aladin PF25460 218 - 303 9.7e-06 Aladin seven-bladed propeller
WD40 PF00400 260 - 301 1.3e-06 WD domain, G-beta repeat
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0012055)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G43770
fragaria_vesca FvH4_4g10290 FvH4_4g10290 FvH4_4g10290 FvH4_4g10290 FvH4_4g10290
malus_domestica MD16G1243600.v1.1
prunus_persica Prupe.1G071000_v2.0.a1
pyrus_communis pycom16g20470
rosa_chinensis RchiOBHm_Chr4g0405641
rosa_laevigata RLG00000008830
rosa_multiflora Rmu_sc0001200.1_g000049
rosa_roxburghii Rroxscaffold_5G00350120
rosa_rugosa Rorug04G0061600
rosa_samantha Rh4AG133000 Rh4BG128000 Rh4CG140700 Rh4DG127400
rosa_wichuraiana Rw4G010780

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 122
Acc16I TGCGCA 1 cut(s) 632
AccB1I GGYRCC 3 cut(s) 133, 518, 801
AccB7I CCANNNNNTGG 1 cut(s) 498
AccI GTMKAC 2 cut(s) 71, 891
AciI CCGC 1 cut(s) 455
AclWI GGATC 4 cut(s) 312, 481, 954, 999
AcoI YGGCCR 2 cut(s) 867, 936
AcsI RAATTY 3 cut(s) 182, 231, 427
AcuI CTGAAG 1 cut(s) 660
AcyI GRCGYC 1 cut(s) 119
AfaI GTAC 1 cut(s) 645
AfiI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 988
AgsI TTSAA 3 cut(s) 659, 818, 832
AjnI CCWGG 1 cut(s) 53
AjuI GAANNNNNNNTTGG 2 cut(s) 284, 316
AluBI AGCT 2 cut(s) 564, 840
AluI AGCT 2 cut(s) 564, 840
Alw26I GTCTC 3 cut(s) 222, 333, 374
AlwI GGATC 4 cut(s) 312, 481, 954, 999
AoxI GGCC 4 cut(s) 56, 98, 867, 936
ApeKI GCWGC 2 cut(s) 145, 931
ApoI RAATTY 3 cut(s) 182, 231, 427
ArsI GACNNNNNNTTYG 2 cut(s) 109, 141
AspLEI GCGC 2 cut(s) 633, 759
AspS9I GGNCC 3 cut(s) 50, 98, 452
AsuHPI GGTGA 2 cut(s) 38, 837
AvaII GGWCC 2 cut(s) 50, 452
BaeGI GKGCMC 1 cut(s) 804
BanI GGYRCC 3 cut(s) 133, 518, 801
BanII GRGCYC 1 cut(s) 983
BbsI GAAGAC 1 cut(s) 957
BbvI GCAGC 2 cut(s) 132, 918
BccI CCATC 7 cut(s) 317, 397, 476, 530, 695, 845, 880
BceAI ACGGC 1 cut(s) 882
BciT130I CCWGG 1 cut(s) 55
BciVI GTATCC 1 cut(s) 895
BcoDI GTCTC 3 cut(s) 222, 333, 374
BfmI CTRYAG 1 cut(s) 42
BfuI GTATCC 1 cut(s) 895
BisI GCNGC 2 cut(s) 146, 932
BlsI GCNGC 2 cut(s) 147, 933
BmcAI AGTACT 1 cut(s) 645
Bme1390I CCNGG 1 cut(s) 55
Bme18I GGWCC 2 cut(s) 50, 452
BmgT120I GGNCC 3 cut(s) 50, 98, 452
BmiI GGNNCC 4 cut(s) 52, 135, 520, 803
BmrFI CCNGG 1 cut(s) 55
BmsI GCATC 5 cut(s) 101, 218, 562, 584, 927
BpiI GAAGAC 1 cut(s) 957
BsaHI GRCGYC 1 cut(s) 119
BsaI GGTCTC 2 cut(s) 222, 333
BsaJI CCNNGG 1 cut(s) 53
BsaWI WCCGGW 1 cut(s) 194
Bsc4I CCNNNNNNNGG 4 cut(s) 23, 95, 498, 988
Bse118I RCCGGY 2 cut(s) 869, 934
Bse1I ACTGG 4 cut(s) 157, 317, 345, 948
BseBI CCWGG 1 cut(s) 55
BseDI CCNNGG 1 cut(s) 53
BseGI GGATG 5 cut(s) 379, 436, 522, 577, 891
BseLI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 988
BseMII CTCAG 2 cut(s) 344, 1023
BseNI ACTGG 4 cut(s) 157, 317, 345, 948
BseSI GKGCMC 1 cut(s) 804
BseX3I CGGCCG 1 cut(s) 867
BseXI GCAGC 2 cut(s) 132, 918
Bsh1285I CGRYCG 1 cut(s) 870
BshFI GGCC 4 cut(s) 58, 100, 869, 938
BshNI GGYRCC 3 cut(s) 133, 518, 801
BsiEI CGRYCG 1 cut(s) 870
BsiSI CCGG 3 cut(s) 195, 870, 935
BslFI GGGAC 2 cut(s) 36, 638
BslI CCNNNNNNNGG 4 cut(s) 23, 95, 498, 988
BsmAI GTCTC 3 cut(s) 222, 333, 374
BsmBI CGTCTC 1 cut(s) 374
BsmFI GGGAC 2 cut(s) 36, 638
BsmI GAATGC 2 cut(s) 263, 298
BsnI GGCC 4 cut(s) 58, 100, 869, 938
Bso31I GGTCTC 2 cut(s) 222, 333
Bsp1286I GDGCHC 2 cut(s) 804, 983
Bsp143I GATC 4 cut(s) 304, 473, 946, 991
BspACI CCGC 1 cut(s) 455
BspANI GGCC 4 cut(s) 58, 100, 869, 938
BspCNI CTCAG 2 cut(s) 343, 1024
BspLI GGNNCC 4 cut(s) 52, 135, 520, 803
BspPI GGATC 4 cut(s) 312, 481, 954, 999
BspT107I GGYRCC 3 cut(s) 133, 518, 801
BspTNI GGTCTC 2 cut(s) 222, 333
BsrFI RCCGGY 2 cut(s) 869, 934
BsrI ACTGG 4 cut(s) 157, 317, 345, 948
BssAI RCCGGY 2 cut(s) 869, 934
BssECI CCNNGG 1 cut(s) 53
BssMI GATC 4 cut(s) 304, 473, 946, 991
BssNI GRCGYC 1 cut(s) 119
Bst2UI CCWGG 1 cut(s) 55
Bst4CI ACNGT 2 cut(s) 202, 361
Bst6I CTCTTC 1 cut(s) 421
BstACI GRCGYC 1 cut(s) 119
BstAPI GCANNNNNTGC 1 cut(s) 741
BstC8I GCNNGC 3 cut(s) 85, 871, 936
BstDEI CTNAG 2 cut(s) 330, 1032
BstEII GGTNACC 1 cut(s) 843
BstF5I GGATG 5 cut(s) 379, 436, 522, 577, 891
BstHHI GCGC 2 cut(s) 633, 759
BstKTI GATC 4 cut(s) 307, 476, 949, 994
BstMAI GTCTC 3 cut(s) 222, 333, 374
BstMBI GATC 4 cut(s) 304, 473, 946, 991
BstMCI CGRYCG 1 cut(s) 870
BstMWI GCNNNNNNNGC 2 cut(s) 89, 741
BstNI CCWGG 1 cut(s) 55
BstPI GGTNACC 1 cut(s) 843
BstSCI CCNGG 1 cut(s) 53
BstSFI CTRYAG 1 cut(s) 42
BstSLI GKGCMC 1 cut(s) 804
BstV1I GCAGC 2 cut(s) 132, 918
BstV2I GAAGAC 1 cut(s) 957
BstX2I RGATCY 4 cut(s) 304, 473, 946, 991
BstXI CCANNNNNNTGG 1 cut(s) 61
BstYI RGATCY 4 cut(s) 304, 473, 946, 991
BstZI CGGCCG 1 cut(s) 867
BsuI GTATCC 1 cut(s) 895
BsuRI GGCC 4 cut(s) 58, 100, 869, 938
BtsCI GGATG 5 cut(s) 379, 436, 522, 577, 891
BtsIMutI CAGTG 3 cut(s) 310, 475, 941
Cac8I GCNNGC 3 cut(s) 85, 871, 936
CfoI GCGC 2 cut(s) 633, 759
Cfr10I RCCGGY 2 cut(s) 869, 934
Cfr13I GGNCC 3 cut(s) 50, 98, 452
CseI GACGC 1 cut(s) 924
Csp6I GTAC 1 cut(s) 644
CviAII CATG 4 cut(s) 142, 251, 271, 369
CviQI GTAC 1 cut(s) 644
DdeI CTNAG 2 cut(s) 330, 1032
DpnI GATC 4 cut(s) 306, 475, 948, 993
DpnII GATC 4 cut(s) 304, 473, 946, 991
DraI TTTAAA 1 cut(s) 279
EaeI YGGCCR 2 cut(s) 867, 936
EagI CGGCCG 1 cut(s) 867
Eam1104I CTCTTC 1 cut(s) 421
EarI CTCTTC 1 cut(s) 421
EclXI CGGCCG 1 cut(s) 867
Eco24I GRGCYC 1 cut(s) 983
Eco31I GGTCTC 2 cut(s) 222, 333
Eco47I GGWCC 2 cut(s) 50, 452
Eco52I CGGCCG 1 cut(s) 867
Eco57I CTGAAG 1 cut(s) 660
Eco91I GGTNACC 1 cut(s) 843
EcoO65I GGTNACC 1 cut(s) 843
EcoRI GAATTC 1 cut(s) 427
EcoRII CCWGG 1 cut(s) 53
EcoT22I ATGCAT 1 cut(s) 577
EcoT38I GRGCYC 1 cut(s) 983
Esp3I CGTCTC 1 cut(s) 374
FaeI CATG 4 cut(s) 145, 254, 274, 372
FaqI GGGAC 2 cut(s) 36, 638
FatI CATG 4 cut(s) 141, 250, 270, 368
FauNDI CATATG 1 cut(s) 896
FblI GTMKAC 2 cut(s) 71, 891
Fnu4HI GCNGC 2 cut(s) 146, 932
FokI GGATG 5 cut(s) 386, 423, 509, 584, 898
FriOI GRGCYC 1 cut(s) 983
Fsp4HI GCNGC 2 cut(s) 146, 932
FspI TGCGCA 1 cut(s) 632
GlaI GCGC 2 cut(s) 632, 758
GluI GCNGC 2 cut(s) 146, 932
HaeIII GGCC 4 cut(s) 58, 100, 869, 938
HapII CCGG 3 cut(s) 195, 870, 935
HgaI GACGC 1 cut(s) 924
HhaI GCGC 2 cut(s) 633, 759
Hin1I GRCGYC 1 cut(s) 119
Hin1II CATG 4 cut(s) 145, 254, 274, 372
Hin6I GCGC 2 cut(s) 631, 757
HinP1I GCGC 2 cut(s) 631, 757
HinfI GANTC 2 cut(s) 694, 958
HpaII CCGG 3 cut(s) 195, 870, 935
HphI GGTGA 2 cut(s) 38, 837
Hpy166II GTNNAC 2 cut(s) 72, 892
Hpy188I TCNGA 8 cut(s) 333, 447, 478, 571, 580, 717, 880, 1033
Hpy188III TCNNGA 6 cut(s) 221, 350, 536, 668, 698, 912
Hpy8I GTNNAC 2 cut(s) 72, 892
Hpy99I CGWCG 1 cut(s) 918
HpyAV CCTTC 1 cut(s) 791
HpyCH4III ACNGT 2 cut(s) 202, 361
HpyCH4IV ACGT 1 cut(s) 119
HpyCH4V TGCA 7 cut(s) 7, 92, 261, 575, 735, 744, 767
HpyF10VI GCNNNNNNNGC 2 cut(s) 89, 741
HpyF3I CTNAG 2 cut(s) 330, 1032
HpySE526I ACGT 1 cut(s) 119
Hsp92I GRCGYC 1 cut(s) 119
Hsp92II CATG 4 cut(s) 145, 254, 274, 372
HspAI GCGC 2 cut(s) 631, 757
KroI GCCGGC 2 cut(s) 869, 934
KroNI GCCGGC 2 cut(s) 871, 936
Kzo9I GATC 4 cut(s) 304, 473, 946, 991
LmnI GCTCC 1 cut(s) 19
Lsp1109I GCAGC 2 cut(s) 132, 918
LweI GCATC 5 cut(s) 101, 218, 562, 584, 927
MaeII ACGT 1 cut(s) 119
MaeIII GTNAC 2 cut(s) 843, 862
MalI GATC 4 cut(s) 306, 475, 948, 993
MboI GATC 4 cut(s) 304, 473, 946, 991
MboII GAAGA 4 cut(s) 299, 408, 704, 957
MflI RGATCY 4 cut(s) 304, 473, 946, 991
MhlI GDGCHC 2 cut(s) 804, 983
MluCI AATT 4 cut(s) 182, 231, 393, 427
MlyI GAGTC 2 cut(s) 703, 967
MmeI TCCRAC 1 cut(s) 282
MnlI CCTC 6 cut(s) 16, 124, 443, 468, 507, 590
Mph1103I ATGCAT 1 cut(s) 577
MroNI GCCGGC 2 cut(s) 869, 934
MseI TTAA 4 cut(s) 186, 278, 396, 615
MslI CAYNNNNRTG 2 cut(s) 162, 291
MspI CCGG 3 cut(s) 195, 870, 935
MspR9I CCNGG 1 cut(s) 55
Mva1269I GAATGC 2 cut(s) 263, 298
MvaI CCWGG 1 cut(s) 55
MwoI GCNNNNNNNGC 2 cut(s) 89, 741
NaeI GCCGGC 2 cut(s) 871, 936
NdeI CATATG 1 cut(s) 896
NdeII GATC 4 cut(s) 304, 473, 946, 991
NgoMIV GCCGGC 2 cut(s) 869, 934
NlaIII CATG 4 cut(s) 145, 254, 274, 372
NlaIV GGNNCC 4 cut(s) 52, 135, 520, 803
NmuCI GTSAC 2 cut(s) 843, 862
NsbI TGCGCA 1 cut(s) 632
NsiI ATGCAT 1 cut(s) 577
PctI GAATGC 2 cut(s) 263, 298
PdiI GCCGGC 2 cut(s) 871, 936
PflMI CCANNNNNTGG 1 cut(s) 498
PkrI GCNGC 2 cut(s) 147, 933
PleI GAGTC 2 cut(s) 702, 966
PpsI GAGTC 2 cut(s) 702, 966
Psp6I CCWGG 1 cut(s) 53
PspEI GGTNACC 1 cut(s) 843
PspGI CCWGG 1 cut(s) 53
PspN4I GGNNCC 4 cut(s) 52, 135, 520, 803
PspPI GGNCC 3 cut(s) 50, 98, 452
PsuI RGATCY 4 cut(s) 304, 473, 946, 991
RsaI GTAC 1 cut(s) 645
RsaNI GTAC 1 cut(s) 644
RseI CAYNNNNRTG 2 cut(s) 162, 291
SaqAI TTAA 4 cut(s) 186, 278, 396, 615
SatI GCNGC 2 cut(s) 146, 932
Sau3AI GATC 4 cut(s) 304, 473, 946, 991
Sau96I GGNCC 3 cut(s) 50, 98, 452
ScaI AGTACT 1 cut(s) 645
SchI GAGTC 2 cut(s) 703, 967
ScrFI CCNGG 1 cut(s) 55
SduI GDGCHC 2 cut(s) 804, 983
SetI ASST 8 cut(s) 122, 566, 601, 621, 685, 842, 850, 864
SfaNI GCATC 5 cut(s) 101, 218, 562, 584, 927
SfcI CTRYAG 1 cut(s) 42
SinI GGWCC 2 cut(s) 50, 452
SmiMI CAYNNNNRTG 2 cut(s) 162, 291
Sse9I AATT 4 cut(s) 182, 231, 393, 427
SsiI CCGC 1 cut(s) 455
StyD4I CCNGG 1 cut(s) 53
TaaI ACNGT 2 cut(s) 202, 361
TaiI ACGT 1 cut(s) 122
TaqI TCGA 1 cut(s) 913
TasI AATT 4 cut(s) 182, 231, 393, 427
TatI WGTACW 1 cut(s) 643
Tru1I TTAA 4 cut(s) 186, 278, 396, 615
Tru9I TTAA 4 cut(s) 186, 278, 396, 615
TscAI CASTG 3 cut(s) 317, 475, 948
TseFI GTSAC 2 cut(s) 843, 862
TseI GCWGC 2 cut(s) 145, 931
Tsp45I GTSAC 2 cut(s) 843, 862
TspDTI ATGAA 4 cut(s) 194, 239, 259, 408
TspRI CASTG 3 cut(s) 317, 475, 948
Van91I CCANNNNNTGG 1 cut(s) 498
VpaK11BI GGWCC 2 cut(s) 50, 452
XapI RAATTY 3 cut(s) 182, 231, 427
XmiI GTMKAC 2 cut(s) 71, 891
ZraI GACGTC 1 cut(s) 120
ZrmI AGTACT 1 cut(s) 645
Zsp2I ATGCAT 1 cut(s) 577
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.